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This page was generated on 2022-01-27 11:08:08 -0500 (Thu, 27 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4167
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4062
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4004
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4121
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for TFutils on riesling1


To the developers/maintainers of the TFutils package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TFutils.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1943/2077HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TFutils 1.15.1  (landing page)
Vincent Carey
Snapshot Date: 2022-01-26 13:55:18 -0500 (Wed, 26 Jan 2022)
git_url: https://git.bioconductor.org/packages/TFutils
git_branch: master
git_last_commit: 6dccfdd
git_last_commit_date: 2021-11-21 01:00:28 -0500 (Sun, 21 Nov 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    NA  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'Rsamtools' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: TFutils
Version: 1.15.1
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TFutils.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings TFutils_1.15.1.tar.gz
StartedAt: 2022-01-26 20:18:48 -0500 (Wed, 26 Jan 2022)
EndedAt: 2022-01-26 20:22:45 -0500 (Wed, 26 Jan 2022)
EllapsedTime: 237.4 seconds
RetCode: 0
Status:   OK  
CheckDir: TFutils.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TFutils.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings TFutils_1.15.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/TFutils.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'TFutils/DESCRIPTION' ... OK
* this is package 'TFutils' version '1.15.1'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'TFutils' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data      3.5Mb
    lambert   1.4Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
fimo_granges : proctext: warning in read.delim(con, h = FALSE,
  stringsAsFactors = FALSE, sep = "\t"): partial argument match of 'h'
  to 'header'
setupHIZE: warning in read.delim(txtfn, sep = "\t", skip = 3, h =
  FALSE, stringsAsFactors = FALSE): partial argument match of 'h' to
  'header'
directHitsInCISBP: no visible binding for global variable
  'DISEASE.TRAIT'
directHitsInCISBP: no visible binding for global variable 'MAPPED_GENE'
directHitsInCISBP: no visible binding for global variable 'cisbpTFcat'
directHitsInCISBP: no visible binding for global variable 'HGNC'
directHitsInCISBP: no visible binding for global variable 'Family_Name'
fimo_granges: no visible global function definition for 'rowRanges<-'
fimo_granges: no visible global function definition for 'reduceByRange'
fimo_granges : <anonymous>: no visible global function definition for
  'seqinfo<-'
tffamCirc.prep: no visible binding for global variable 'TF family'
tffamCirc.prep: no visible binding for global variable 'TFfamily'
tffamCirc.prep: no visible binding for global variable 'Transcription
  factor'
topTraitsOfTargets: no visible global function definition for 'mcols'
topTraitsOfTargets: no visible binding for global variable
  'DISEASE.TRAIT'
Undefined global functions or variables:
  DISEASE.TRAIT Family_Name HGNC MAPPED_GENE TF family TFfamily
  Transcription factor cisbpTFcat mcols reduceByRange rowRanges<-
  seqinfo<-
Consider adding
  importFrom("base", "factor")
  importFrom("stats", "family")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... NOTE
  Note: found 62 marked UTF-8 strings
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
tffamCirc.plot     25.00   0.26   25.36
tffamCirc.prep     14.91   0.00   14.90
topTraitsOfTargets  8.64   0.16    8.79
fimo16              7.25   0.43    7.67
genemodForGviz      5.34   0.42    5.77
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/TFutils.Rcheck/00check.log'
for details.



Installation output

TFutils.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL TFutils
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'TFutils' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'TFutils'
    finding HTML links ... done
    HGNCmap                                 html  
    TFCatalog-class                         html  
    TFCatalog                               html  
    TFtargs                                 html  
    URL_s3_tf                               html  
    anchor_pmids                            html  
    browse_gotf_main                        html  
    browse_humantfs_main                    html  
    browse_lambert_gwaslinks                html  
    browse_lambert_main                     html  
    cisbpTFcat                              html  
    cisbpTFcat_2.0                          html  
    defaultCircosParms                      html  
    demo_fimo_granges                       html  
    directHitsInCISBP                       html  
    encode690                               html  
    fimo16                                  html  
    fimoMap                                 html  
    fimo_granges                            html  
    genemodForGviz                          html  
    genemodelDF                             html  
    get_rslocs_38                           html  
    grabTab                                 html  
    gwascat_hg19_chr17                      html  
    hocomoco.mono                           html  
    hocomoco.mono.sep2018                   html  
    importFIMO                              html  
    importFIMO_local_split                  html  
    lambert_snps                            html  
    metadata_tf                             html  
    named_tf                                html  
    retrieve_gotf_main                      html  
    retrieve_humantfs_main                  html  
    retrieve_lambert_main                   html  
    seqinfo_hg19_chr17                      html  
    setupHIZE                               html  
    show-TFCatalog-method                   html  
    tffamCirc.plot                          html  
    tffamCirc.prep                          html  
    tfhash                                  html  
    tftColl                                 html  
    tftCollMap                              html  
    topTraitsOfTargets                      html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (TFutils)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'MicrobiotaProcess' is missing or broken
 done

Tests output

TFutils.Rcheck/tests/testthat.Rout


R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(TFutils)

> 
> test_check("TFutils")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 5 ]
> 
> 
> proc.time()
   user  system elapsed 
  13.45    1.20   14.64 

Example timings

TFutils.Rcheck/TFutils-Ex.timings

nameusersystemelapsed
HGNCmap000
TFCatalog0.230.010.25
TFtargs000
URL_s3_tf000
anchor_pmids000
browse_gotf_main000
browse_humantfs_main000
browse_lambert_gwaslinks000
browse_lambert_main000
cisbpTFcat0.030.000.04
cisbpTFcat_2.00.450.000.45
defaultCircosParms0.000.020.01
demo_fimo_granges000
directHitsInCISBP0.130.010.15
encode6900.040.000.04
fimo167.250.437.67
fimoMap000
fimo_granges000
genemodForGviz5.340.425.77
genemodelDF0.100.000.09
get_rslocs_38000
grabTab0.190.000.19
gwascat_hg19_chr170.040.000.04
hocomoco.mono000
hocomoco.mono.sep2018000
importFIMO0.030.010.05
importFIMO_local_split0.000.020.02
lambert_snps0.240.030.26
metadata_tf0.010.000.02
named_tf0.000.020.01
retrieve_gotf_main000
retrieve_humantfs_main000
retrieve_lambert_main000
seqinfo_hg19_chr170.000.000.02
tffamCirc.plot25.00 0.2625.36
tffamCirc.prep14.91 0.0014.90
tfhash0.500.310.82
tftColl0.250.000.25
tftCollMap000
topTraitsOfTargets8.640.168.79